3-114232449-C-G

Variant names:

• chr3-114232449-C-G
• rs905568
• ENST00000473625.1:n.573G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000473625.1(ATOSBP1):​n.573G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 478,516 control chromosomes in the GnomAD database, including 82,672 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.62 (29801 hom., cov: 32)
  • Exomes 𝑓: 0.56 (52871 hom.)
• Consequence: ATOSBP1 ENST00000473625.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 11 publications found

Genes affected

ATOSBP1 (HGNC:54597): (ATOSB pseudogene 1)

ENSG00000241490 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473625.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATOSBP1	ENST00000473625.1	TSL:6	n.573G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000241490	ENST00000481773.2	TSL:3	n.239-893C>G		intron	N/A
	ENSG00000241490	ENST00000493033.1	TSL:2	n.161-893C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93438 AN: 151904 Hom.: 29753 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.626

GnomAD4 exome AF: 0.564 AC: 184109 AN: 326496 Hom.: 52871 Cov.: 0 AF XY: 0.571 AC XY: 100161 AN XY: 175386

African (AFR) AF: 0.797 AC: 6078 AN: 7630

American (AMR) AF: 0.558 AC: 8430 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 6278 AN: 8892

East Asian (EAS) AF: 0.556 AC: 9086 AN: 16342

South Asian (SAS) AF: 0.680 AC: 22582 AN: 33232

European-Finnish (FIN) AF: 0.557 AC: 15641 AN: 28100

Middle Eastern (MID) AF: 0.746 AC: 2177 AN: 2920

European-Non Finnish (NFE) AF: 0.526 AC: 103111 AN: 195950

Other (OTH) AF: 0.585 AC: 10726 AN: 18330

GnomAD4 genome AF: 0.615 AC: 93547 AN: 152020 Hom.: 29801 Cov.: 32 AF XY: 0.617 AC XY: 45861 AN XY: 74310

African (AFR) AF: 0.792 AC: 32878 AN: 41494

American (AMR) AF: 0.562 AC: 8585 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2762 AN: 5138

South Asian (SAS) AF: 0.686 AC: 3311 AN: 4830

European-Finnish (FIN) AF: 0.554 AC: 5856 AN: 10574

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35812 AN: 67908

Other (OTH) AF: 0.628 AC: 1328 AN: 2114

Alfa AF: 0.414 Hom.: 980

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.7
DANN	Benign	0.59
PhyloP100		0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs905568; hg19: chr3-113951296; COSMIC: COSV57361870;